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Mercury in PDB 1dkp: Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge

Enzymatic activity of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge

All present enzymatic activity of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge, PDB code: 1dkp was solved by D.Lim, S.Golovan, C.W.Forsberg, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.573, 75.127, 90.393, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.7

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge (pdb code 1dkp). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge, PDB code: 1dkp:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 1dkp

Go back to Mercury Binding Sites List in 1dkp
Mercury binding site 1 out of 4 in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg500

b:34.4
occ:1.00
 ND1 A:HIS113 2.6 33.2 1.0
O A:HOH613 2.8 25.7 1.0
O A:TYR289 2.9 42.9 1.0
O A:HOH820 3.1 50.3 1.0
CG A:HIS113 3.4 32.8 1.0
CB A:HIS113 3.4 28.3 1.0
CE1 A:HIS113 3.6 34.9 1.0
C A:TYR289 4.0 42.4 1.0
CA A:HIS113 4.1 27.3 1.0
O A:HOH798 4.4 34.4 1.0
CA A:GLY290 4.6 43.0 1.0
CD2 A:HIS113 4.6 36.1 1.0
NE2 A:HIS113 4.7 38.4 1.0
N A:GLY290 4.7 40.8 1.0
CG2 A:THR111 4.8 31.5 1.0
CA A:TYR289 5.0 40.5 1.0

Mercury binding site 2 out of 4 in 1dkp

Go back to Mercury Binding Sites List in 1dkp
Mercury binding site 2 out of 4 in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg501

b:37.4
occ:0.60
 NE2 A:HIS282 2.6 53.3 1.0
O A:LEU293 2.7 40.9 1.0
O A:HOH866 2.8 50.6 1.0
O A:HOH865 2.9 44.8 1.0
OE1 A:GLN287 3.1 58.9 1.0
OE1 A:GLN285 3.1 70.4 1.0
CD2 A:HIS282 3.5 53.8 1.0
CG A:GLN285 3.5 66.1 1.0
C A:LEU293 3.5 41.8 1.0
CE1 A:HIS282 3.6 56.0 1.0
CD A:GLN285 3.7 70.5 1.0
CB A:LEU293 4.0 41.1 1.0
CD A:GLN287 4.2 62.4 1.0
OG1 A:THR277 4.3 46.0 1.0
N A:PRO294 4.3 41.3 1.0
CA A:LEU293 4.3 42.7 1.0
CD A:PRO294 4.4 35.0 1.0
O A:GLN285 4.5 60.7 1.0
O A:PRO283 4.5 50.7 1.0
N A:LEU293 4.6 43.8 1.0
CG A:HIS282 4.6 52.4 1.0
ND1 A:HIS282 4.6 54.7 1.0
CB A:GLN287 4.8 53.0 1.0
N A:GLN285 4.9 58.9 1.0
CG A:GLN287 4.9 60.0 1.0
CB A:GLN285 4.9 63.0 1.0

Mercury binding site 3 out of 4 in 1dkp

Go back to Mercury Binding Sites List in 1dkp
Mercury binding site 3 out of 4 in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg502

b:39.7
occ:0.26
 HG A:HG503 1.7 30.7 0.1
NE2 A:HIS250 2.6 26.3 1.0
OD2 A:ASP325 2.8 25.1 1.0
NH1 A:ARG16 2.9 25.2 1.0
OE2 A:GLU219 3.0 33.9 1.0
OD1 A:ASP304 3.0 32.9 1.0
CD A:GLU219 3.2 32.4 1.0
O24 A:IHP550 3.2 41.8 0.8
CZ A:ARG16 3.2 27.1 1.0
OE1 A:GLU219 3.3 31.0 1.0
NH2 A:ARG16 3.3 25.7 1.0
CE1 A:HIS250 3.5 27.4 1.0
CD2 A:HIS250 3.6 21.6 1.0
O A:THR327 3.6 28.1 1.0
CG A:ASP325 3.6 24.7 1.0
OD1 A:ASP325 3.7 29.2 1.0
CG A:ASP304 4.0 32.3 1.0
CB A:ASP304 4.0 27.7 1.0
NE A:ARG16 4.1 23.8 1.0
OG1 A:THR327 4.2 27.7 1.0
CG A:GLU219 4.2 23.7 1.0
C A:THR327 4.5 26.0 1.0
ND1 A:HIS250 4.5 30.4 1.0
P4 A:IHP550 4.6 39.2 0.8
CG A:HIS250 4.6 27.1 1.0
CZ A:PHE254 4.8 26.1 1.0
CD A:ARG16 4.8 22.2 1.0
CB A:GLU219 4.9 23.1 1.0
O34 A:IHP550 4.9 41.7 0.8

Mercury binding site 4 out of 4 in 1dkp

Go back to Mercury Binding Sites List in 1dkp
Mercury binding site 4 out of 4 in the Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Phytate Complex of Escherichia Coli Phytase at pH 6.6. Phytate Is Bound with Its 3-Phosphate in the Active Site. HG2+ Cation Acts As An Intermolecular Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg503

b:30.7
occ:0.15
 HG A:HG502 1.7 39.7 0.3
OG1 A:THR327 2.6 27.7 1.0
NE2 A:HIS250 2.7 26.3 1.0
OD1 A:ASP325 2.9 29.2 1.0
O A:THR327 3.0 28.1 1.0
OD2 A:ASP325 3.1 25.1 1.0
OD1 A:ASP304 3.3 32.9 1.0
CG A:ASP325 3.4 24.7 1.0
CD2 A:HIS250 3.4 21.6 1.0
CB A:ASP304 3.6 27.7 1.0
O A:HOH604 3.7 26.8 1.0
C A:THR327 3.7 26.0 1.0
CB A:THR327 3.8 25.5 1.0
NH1 A:ARG16 3.8 25.2 1.0
CG A:ASP304 3.9 32.3 1.0
CE1 A:HIS250 3.9 27.4 1.0
CA A:THR327 4.2 25.7 1.0
CZ A:ARG16 4.2 27.1 1.0
OE2 A:GLU219 4.2 33.9 1.0
CZ A:PHE254 4.3 26.1 1.0
N A:THR327 4.3 21.9 1.0
O24 A:IHP550 4.4 41.8 0.8
CE2 A:PHE254 4.4 26.1 1.0
CE1 A:PHE254 4.6 29.3 1.0
CG A:HIS250 4.6 27.1 1.0
NH2 A:ARG16 4.7 25.7 1.0
N A:PRO328 4.7 26.5 1.0
CD A:GLU219 4.7 32.4 1.0
NE A:ARG16 4.8 23.8 1.0
CD2 A:PHE254 4.8 27.6 1.0
OE1 A:GLU219 4.8 31.0 1.0
ND1 A:HIS250 4.9 30.4 1.0
CB A:ASP325 4.9 24.6 1.0
CG2 A:THR327 5.0 22.2 1.0
CD1 A:PHE254 5.0 27.3 1.0
CA A:ASP304 5.0 25.8 1.0

Reference:

D.Lim, S.Golovan, C.W.Forsberg, Z.Jia. Crystal Structures of Escherichia Coli Phytase and Its Complex with Phytate. Nat.Struct.Biol. V. 7 108 2000.
ISSN: ISSN 1072-8368
PubMed: 10655611
DOI: 10.1038/72371
Page generated: Sat Aug 10 23:34:28 2024

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